Te Raupapatanga Ira Katoa o te Tipu/Kararehe
Ngā Āhuatanga Ratonga
Nō nā tata nei
He tino whai hua tēnei tikanga mō ngā ira uaua pērā i ngā ira he nui te heterozygosity, ngā rohe tāruarua, ngā ira polypoloid, ngā ihirangi CG rerekē, me ētahi atu.
Mā tā mātou otinga kotahi-mutu ka whakaratohia he ratonga raupapatanga whakauru me te tātaritanga koiora-pārongo e tuku ana i tētahi ira kua oti te hanga kounga teitei. Mā te rangahau ira tuatahi me Illumina ka whakaratohia he whakatau tata mō te rahi me te uaua o te ira, ā, ka whakamahia ēnei mōhiohio hei ārahi i te taahiraa e whai ake nei o te raupapatanga roa-pānui me PacBio HiFi, ā, ka whai ake konō nāte huihuinga o ngā hononga. Mā te whakamahinga o te huihuinga HiC i muri mai ka taea te here i ngā hononga ki te ira, ka whiwhi i te huihuinga taumata-chromosome. Hei whakamutunga, ka tohua te ira mā te matapae ira me te raupapa i ngā ira kua whakaatuhia, me te whakamahi i ngā transcriptome me ngā pānui poto me ngā pānui roa.
-- Te whakaurunga o ngā ratonga raupapatanga maha me ngā ratonga mōhiohio koiora ki roto i tētahi otinga kotahi-mutuRatonga e tika ana mō te hanga pukapuka hou
-- ngā ira, te whakapainga rānei o ngā ira tohutoro o nāianei mō ngā momo e hiahiatia ana.
Te raupapatanga anō
-- Ka taea te whakarite whare pukapuka hei paerewa, hei kore rānei he PCR
-- E wātea ana i roto i ngā tūāpapa raupapatanga e 4: Illumina NovaSeq, MGI T7, Nanopore Promethion P48, PacBio Revio rānei.
-- Te tātaritanga koiora-pūtaiao e arotahi ana ki te karangatanga rerekē: SNP, InDel, SV me CNV
Ngā Painga Ratonga
●Te Tohungatanga Whānui me te Rēkoata WhakaputangaMōnō nāI roto i ā mātou ratonga, he nui ngā wheako kua kohia e mātou ki te whakahiato ira kounga teitei o ngā momo kanorau, tae atu ki ngā ira takirua me ngā ira tino uaua o ngā momo polyploid me ngā momo allopolyploid. Mai i te tau 2018, kua whai wāhi mātou ki te neke atu i te 300 ngā whakaputanga whai pānga nui, ā, neke atu i te 20 o ēnei kua whakaputaina ki roto i te Nature Genetics. I te raupapatanga anō o te ira, i kohia e mātou neke atu i te 1000 ngā momo, ā, i hua ake ai he neke atu i te 1000 ngā kēhi kua whakaputaina me te tauwehenga pānga tāpiri o neke atu i te 5000.
●Otinga Kotahi-MutuKei tenō nāte raupapatanga, ka whakakotahihia e tā mātou huarahi whakauru ngā hangarau raupapatanga maha me ngā tātaritanga koiora-pārongo ki roto i tētahi rerenga mahi kotahi, ka tukuna he ira kua huihuia kounga teitei.
●I whakaritea kia rite ki ō hiahiaKa taea te whakarite i tā mātou tukanga ratonga, kia taea ai te urutau mō ngā ira me ngā āhuatanga rerekē me ngā hiahia rangahau motuhake.
●He Rōpū Pūtaiao Koiora me te Taiwhanga Tino PūkengaAhakoa mōnō nāte raupapatanga, te raupapatanga anō rānei, he taputapu me te mātauranga matatau tā tā mātou tīma hei whakapūmau i te angitu o te kaupapa. Ka taea tēnei te tautoko i te raupapa o ngā mana pupuri me ngā mana pupuri pūmanawa kua whakawhanakehia e rātou.
● Tautoko Whai muri i te Hokonga:E toru marama te roa o tā mātou whakapau kaha ki te whakaoti i te kaupapa, ā, ka tukuna atu he ratonga whai muri i te hoko mō ngā marama e toru. I tēnei wā, ka tukuna atu e mātou he āwhina ki te rapu raruraru, me ngā wā pātai me ngā whakautu hei whakautu i ngā pātai e pā ana ki ngā hua.
●Tātaritanga Pūtaiao Koiora WhānuiTae atu ki te karangatanga rerekētanga me te tuhipoka mahi.
●He Whakarāpopototanga Whānui mō te RaupapaKa whakamahia e mātou ngā pātengi raraunga maha hei tāpiri i ngā kōrero mō ngā ira me ngā rerekētanga kua tautuhia, me te mahi i te tātari whakarei ake e rite ana, hei whakarato māramatanga mō āu kaupapa rangahau.
Ngā Whakatakotoranga Ratonga
| Ngā momo rerekē hei tautuhi | Rautaki raupapatanga | Hōhonutanga e taunakitia ana |
| SNP me InDel | Illumina NovaSeq PE150 MGI T7 rānei | 10x |
| SV me CNV (kāore i te tino tika) | 30x | |
| SV me CNV (tika ake) | Nanopore Prom P48 | 20x |
| Ngā SNP, ngā Indels, ngā SV me ngā CNV | Arotake PacBio | 10x |
Ngā Whakaritenga Tauira
| Ngā waikawa karihi kiko, ngā waikawa karihi rānei i tangohia | Illumina/MGI | Nanopore | PacBio
| ||
| Ngā whekau kararehe | 0.5-1 karamu | ≥ 3.5 karamu
| ≥ 3.5 karamu
| ||
| Uaua Kararehe | ≥ 5 karamu
| ≥ 5 karamu
| |||
| Toto Mamari | 1.5 mL | ≥ 0.5 mL
| ≥ 5 mL
| ||
| Toto Manu/Ika | ≥ 0.1 mL
| ≥ 0.5 mL
| |||
| Rau Hou - Tipu | 1-2 karamu | ≥ 2 karamu
| ≥ 5 karamu
| ||
| Ngā Pūtau Whakatipu |
| ≥ 1x107
| ≥ 1x108
| ||
| Ngārara kiko ngohengohe/takitahi | 0.5-1 karamu | ≥ 1 karamu
| ≥ 3 karamu
| ||
| DNA i tangohia
| Kukū: ≥ 1 ng/ µL Te nui: ≥ 30 ng He iti, he kore rānei te pirau, te poke rānei
| Te arotahi Te nui
OD260/280
OD260/230
He iti, he kore rānei te pirau, te poke rānei
| ≥ 40 ng/µL 4 µg/pūtau rere/tauira
1.7-2.2
≥1.5 | Te arotahi Te nui
OD260/280
OD260/230
He iti, he kore rānei te pirau, te poke rānei | ≥ 50 ng/µL 10 µg/pūtau rere/tauira
1.7-2.2
1.8-2.5 |
| Te Whakaritenga Whare Pukapuka Kore-PCR: Kukū ≥ 40 ng/ µL Te nui ≥ 500 ng | |||||
Rere Mahi Ratonga
Tukunga tauira
Te tango i te DNA
Te hanganga whare pukapuka
Te raupapatanga
Tātari raraunga
Tukunga raraunga
Nō nā tata neite paipa hangarau koiora
Mena kei te hiahia koe ki te tiro i tētahi tirohanga whānui o ā mātou paipa rerekē mō te huihuinga:
Te tātaritanga koiora-pūtaiao katoa, wehea kia 4 ngā taahiraa:
1. Arotake ira, i runga i te tātaritanga k-mer me ngā pānui NGS.Ka homai he kōrero ki a tātou mō:
- Te whakatau tata i te rahi o te ira
- Te whakatau tata i te heterozygosity
- Te whakatau tata o ngā rohe auau
2. Te Huihuinga Ira me te PacBio HiFi.Mā te whakamahi i ngā pānui roa ka puta mai:
- Nō nā tata neihuihuinga
- Aromatawai huihuinga: tae atu ki te tātaritanga BUSCO mō te otinga o te ira me te mahere whakamuri o ngā pānui NGS me PacBio HiFi
3. Huinga Hi-C.Kia oti te huihuinga, mā te whai mōhiohio mō te hanganga 3D o te ira ka hohonu ake te mōhiotanga, ka whakarei ake hoki i te ira tohutoro e hangaia ana e tātou.
- Te QC o te whare pukapuka Hi-C hei whakatau tata i ngā taunekeneke Hi-C tika.
- Huihuinga Hi-C. Ka whakarōpūhia ngā hononga ki ngā rōpū, ā, ka whai ake ko te raupapa hononga ki roto i ia rōpū me te tuku i te aronga hononga.
- Aromatawai Hi-C
4. Whakamōhiotanga ira:
- Matapae RNA kore-waehere
- Te tautuhi i ngā raupapatanga tāruarua (ngā whakawhiti me ngā tāruarua takirua)
- Matapae ira
- Nō nā tata neingā rauropi ab initio
- I runga i te homology
- I runga i te transcriptome, me ngā pānui roa me ngā pānui poto: ko ngā pānuinō nāi huihuia, i maheretia rānei ki te tauira ira
- He whakamārama i ngā ira i matapaetia me ngā pātengi raraunga maha
Te raupapatanga anōte paipa hangarau koiora
Kei roto ko te tātaritanga e whai ake nei:
- Mana Whakahaere Kounga Raraunga Mata
- Ngā tatauranga o te whakahāngaitanga ki te ira tohutoro
- Te tautuhi rerekētanga: SNP, InDel, SV me CNV
- He whakamārama mahi mō ngā momo rerekētanga
Ngā tatauranga o te whakahāngaitanga ki te tohatoha hohonu o te raupapatanga ira tohutoro
Karanga SNP i waenga i ngā tauira maha
Te tautuhi InDel – ngā tatauranga o te roa o InDel i te rohe CDS me te rohe whānui-ira
Te tohatoha rerekētanga puta noa i te ira - Kauwhata Circos
Te whakamārama mahi o ngā ira me ngā rerekētanga kua tautuhia – Gene Ontology
Chai, Q. et al. (2023) 'Ka whakatauhia e te glutathione S-transferase GhTT19 te tae o te rau putiputi mā te whakahaere i te kohikohinga anthocyanin i roto i te miro',Te Hautaka Hangarau Koiora Tipu, 21(2), wh. 433. doi: 10.1111/PBI.13965.
Cheng, H. et al. (2023) 'Ko te ira Hevea brasiliensis mohoao taumata-ira e whakarato ana i ngā taputapu hou mō te whakatipu uri ā-ira me ngā wāhi whai hua hei whakanui ake i te hua rapa',Te Hautaka Hangarau Koiora Tipu, 21(5), wh. 1058–1072. doi: 10.1111/PBI.14018.
Li, C. et al. (2021) 'E whakaatu ana ngā raupapatanga ira i ngā ara marara ā-ao, ā, e whakaatu ana i ngā urutaunga ira honohono i roto i te whanaketanga hōiho moana',Ngā Whakawhitiwhiti Kōrero Taiao, 12(1). doi: 10.1038/S41467-021-21379-X.
Li, Y. et al. (2023) 'Ngā Huringa Ira-Nui e Ārahi Ana ki ngā Huringa Whakapuakitanga Taumata-Ira, te Urutau Taiao, me te Whakapūtanga i roto i te Gayal (Bos frontalis)',Koiora Ngongo me te Whanaketanga, 40(1). doi: 10.1093/MOLBEV/MSAD006.
Tian, T. et al. (2023) 'Te huihuinga ira me te wetewete ira o tētahi ira kānga pakari ātete-tauraki',Ngā Ira Taiao 202355:3, 55(3), api 496–506. doi: 10.1038/s41588-023-01297-y.
Zhang, F. et al. (2023) 'Te whakaatu i te whanaketanga o te hanganga matū o te alkaloid tropane mā te tātari i ngā ira e rua i roto i te whānau Solanaceae',Ngā Whakawhitiwhiti Kōrero Taiao2023 14:1, 14(1), whārangi 1–18. doi: 10.1038/s41467-023-37133-4.
Zeng, T. et al. (2022) 'Mā te tātari i ngā huringa ira me te methylation i roto i ngā heihei taketake Hainamana i roto i te wā ka kitea te tiaki momo',Koiora Whakawhitiwhiti Kōrero, 5(1), wh. 1–12. doi: 10.1038/s42003-022-03907-7.
Ngā rangahau take wero:
Te huihuinga o te telomere-ki-telomere:Fu, A. et al. (2023) 'Ko te huihuinga ira telomere-ki-telomere o te merengi kawa (Momordica charantia L. var. abbreviata Ser.) e whakaatu ana i te whanaketanga o te hua, te hanganga me ngā āhuatanga ira pakari',Rangahau Māra, 10(1). doi: 10.1093/HR/UHAC228.
Te huihuinga Haplotype:Hu, W. et al. (2021) 'E whakaatu ana te ira kua tautuhia e te allele i te rerekētanga biallelic i te wā o te whanaketanga o te manioka',Te tipu ngota, 14(6), api 851–854. doi: 10.1016/j.molp.2021.04.009.
Te huihuinga ira nui:Yuan, J. et al. (2022) 'Te pūtake ira o ngā ira-kiga me ngā ira-kiga o te peony rākau Paeonia ostii',Ngā Whakawhitiwhiti Kōrero Taiao2022 13:1, 13(1), wh. 1–16. doi: 10.1038/s41467-022-35063-1.
Te huihuinga ira polyploid:Zhang, Q. et al. (2022) 'Ngā tirohanga ira ki te whakaiti i ngā ira o te autopolyploid sugarcane Saccharum spontaneum',Ngā Ira Taiao 202254:6, 54(6), api 885–896. doi: 10.1038/s41588-022-01084-1.
